Issues installing from source on macOS Big Sur 11.5.2 about gnn HOT 15 CLOSED

Actually, this is because a file named sampling_spec_pb2.py is missing.

At commit "2101be", they removed the line "tensorflow_gnn/sampler/sampling_spec_pb2.py" from package/move_generated_files.sh. However, this sh file was created at commit "f63576". At this "f63576" commit, the package/BUILD file also included this line "//tensorflow_gnn/sampler:sampling_spec_pb2.py".

Afterwards, they deleted the sampling_spec.py and removed the "sampling_spec_pb2.py" line from file package/move_generated_files.sh at commit "2101be", but forgot to remove it from that BUILD file too. I guess.

As a result, you can just remove the line "//tensorflow_gnn/sampler:sampling_spec_pb2.py" from package/BUILD file (line 17).

from gnn.

I have the same problem on Ubuntu 20.04. It seems like the script is looking for setup.py in a temporary directory that doesn't exist.

from gnn.

@lucky630 Not sure the root cause. Seems that no submodules are included. You may uninstall and reinstall it again. BTW, my bazel version is 4.2.1.

Once installed, for me, the __init__.py in the corresponding directory site-packages/tensorflow_gnn should be as follows:

from tensorflow_gnn.graph import graph_tensor_encode
from tensorflow_gnn.graph import graph_tensor_io
from tensorflow_gnn.graph import graph_tensor_ops
from tensorflow_gnn.graph import graph_tensor_pprint
from tensorflow_gnn.graph import graph_tensor_random
from tensorflow_gnn.graph import keras  # For use as a subpackage.
from tensorflow_gnn.graph import normalization_ops
from tensorflow_gnn.graph import schema_utils
from tensorflow_gnn.graph import schema_validation
from tensorflow_gnn.proto import graph_schema
...

from gnn.

+1

from gnn.

I have the same issue.

from gnn.

As a result, you can just remove the line "//tensorflow_gnn/sampler:sampling_spec_pb2.py" from package/BUILD file (line 17).

still getting error after removing the line from package/BUILD file

from gnn.

As a result, you can just remove the line "//tensorflow_gnn/sampler:sampling_spec_pb2.py" from package/BUILD file (line 17).

still getting error after removing the line from package/BUILD file

You may provide the error log, please. I don't think the same error will arise if you remove the line, because there are no other references to the sampling_spec.py. You can confirm this by executing ag "sampling_spec" in the terminal (ag is a powerful searching tool silversearcher-ag.).

from gnn.

You may provide the error log, please. I don't think the same error will arise if you remove the line, because there are no other references to the sampling_spec.py. You can confirm this by executing ag "sampling_spec" in the terminal (ag is a powerful searching tool silversearcher-ag.).

tensorflow-gnn==0.1.0) (0.4.3) Building wheels for collected packages: tensorflow-gnn Building wheel for tensorflow-gnn (setup.py) ... error ERROR: Failed building wheel for tensorflow-gnn Running setup.py clean for tensorflow-gnn Failed to build tensorflow-gnn Installing collected packages: tensorflow-gnn Running setup.py install for tensorflow-gnn ... error ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/content/tensorflow_gnn/setup.py'"'"'; __file__='"'"'/content/tensorflow_gnn/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-12b9919l/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.9/tensorflow-gnn Check the logs for full command output.

from gnn.

@lucky630 - could you show the full error message and the errors from the logs?

from gnn.

@lucky630 - could you show the full error message and the errors from the logs?

That's the full error that I'm getting. I'm using Google Colab for the installation.
Have installed and Bazel and Graphviz,
python version is 3.9.9 and TensorFlow version is 2.7.0

Processing /content/tensorflow_gnn Preparing metadata (setup.py) ... done Requirement already satisfied: absl-py in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (1.0.0) Requirement already satisfied: apache-beam[gcp]>=2.32 in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (2.34.0) Requirement already satisfied: grpcio in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (1.42.0) Requirement already satisfied: matplotlib in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (3.5.0) Requirement already satisfied: mock in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (4.0.3) Requirement already satisfied: networkx in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (2.6.3) Requirement already satisfied: numpy in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (1.20.3) Requirement already satisfied: protobuf>=3.17 in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (3.19.1) Requirement already satisfied: pyarrow in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (5.0.0) Requirement already satisfied: pygraphviz in /usr/local/lib/python3.9/dist-packages/pygraphviz-1.8rc1.dev0-py3.9-linux-x86_64.egg (from tensorflow-gnn==0.1.0) (1.8rc1.dev0) Requirement already satisfied: scipy in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (1.7.3) Requirement already satisfied: six in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (1.16.0) Requirement already satisfied: tensorflow-cpu>=2.7.0 in /usr/local/lib/python3.9/dist-packages (from tensorflow-gnn==0.1.0) (2.7.0) Requirement already satisfied: future<1.0.0,>=0.18.2 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (0.18.2) Requirement already satisfied: dill<0.3.2,>=0.3.1.1 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (0.3.1.1) Requirement already satisfied: httplib2<0.20.0,>=0.8 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (0.19.1) Requirement already satisfied: pytz>=2018.3 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (2021.3) Requirement already satisfied: crcmod<2.0,>=1.7 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.7) Requirement already satisfied: pymongo<4.0.0,>=3.8.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (3.12.1) Requirement already satisfied: oauth2client<5,>=2.0.1 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (4.1.3) Requirement already satisfied: requests<3.0.0,>=2.24.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (2.26.0) Requirement already satisfied: avro-python3!=1.9.2,<1.10.0,>=1.8.1 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.9.2.1) Requirement already satisfied: orjson<4.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (3.6.4) Requirement already satisfied: hdfs<3.0.0,>=2.1.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (2.6.0) Requirement already satisfied: pydot<2,>=1.2.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.4.2) Requirement already satisfied: fastavro<2,>=0.21.4 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.4.7) Requirement already satisfied: typing-extensions<4,>=3.7.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (3.10.0.2) Requirement already satisfied: python-dateutil<3,>=2.8.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (2.8.2) Requirement already satisfied: google-cloud-spanner<2,>=1.13.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.19.1) Requirement already satisfied: google-cloud-language<2,>=1.3.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.3.0) Requirement already satisfied: google-cloud-pubsub<2,>=0.39.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.7.0) Requirement already satisfied: google-cloud-recommendations-ai<=0.2.0,>=0.1.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (0.2.0) Requirement already satisfied: grpcio-gcp<1,>=0.2.2 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (0.2.2) Requirement already satisfied: google-cloud-bigquery-storage>=2.6.3 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (2.10.1) Requirement already satisfied: google-auth<3,>=1.18.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.35.0) Requirement already satisfied: google-cloud-core<2,>=0.28.1 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.7.2) Requirement already satisfied: cachetools<5,>=3.1.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (4.2.4) Requirement already satisfied: google-cloud-vision<2,>=0.38.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.0.0) Requirement already satisfied: google-apitools<0.5.32,>=0.5.31 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (0.5.31) Requirement already satisfied: google-cloud-bigtable<2,>=0.31.1 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.7.0) Requirement already satisfied: google-cloud-bigquery<3,>=1.6.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (2.30.1) Requirement already satisfied: google-cloud-videointelligence<2,>=1.8.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.16.1) Requirement already satisfied: google-cloud-dlp<2,>=0.12.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.0.0) Requirement already satisfied: google-cloud-datastore<2,>=1.8.0 in /usr/local/lib/python3.9/dist-packages (from apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (1.15.3) Requirement already satisfied: h5py>=2.9.0 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (3.6.0) Requirement already satisfied: keras<2.8,>=2.7.0rc0 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (2.7.0) Requirement already satisfied: wheel<1.0,>=0.32.0 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (0.37.0) Requirement already satisfied: wrapt>=1.11.0 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (1.13.3) Requirement already satisfied: tensorboard~=2.6 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (2.7.0) Requirement already satisfied: tensorflow-estimator<2.8,~=2.7.0rc0 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (2.7.0) Requirement already satisfied: libclang>=9.0.1 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (12.0.0) Requirement already satisfied: termcolor>=1.1.0 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (1.1.0) Requirement already satisfied: astunparse>=1.6.0 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (1.6.3) Requirement already satisfied: flatbuffers<3.0,>=1.12 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (2.0) Requirement already satisfied: gast<0.5.0,>=0.2.1 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (0.4.0) Requirement already satisfied: tensorflow-io-gcs-filesystem>=0.21.0 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (0.22.0) Requirement already satisfied: google-pasta>=0.1.1 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (0.2.0) Requirement already satisfied: opt-einsum>=2.3.2 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (3.3.0) Requirement already satisfied: keras-preprocessing>=1.1.1 in /usr/local/lib/python3.9/dist-packages (from tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (1.1.2) Requirement already satisfied: setuptools-scm>=4 in /usr/local/lib/python3.9/dist-packages (from matplotlib->tensorflow-gnn==0.1.0) (6.3.2) Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.9/dist-packages (from matplotlib->tensorflow-gnn==0.1.0) (21.3) Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.9/dist-packages (from matplotlib->tensorflow-gnn==0.1.0) (1.3.2) Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.9/dist-packages (from matplotlib->tensorflow-gnn==0.1.0) (4.28.2) Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.9/dist-packages (from matplotlib->tensorflow-gnn==0.1.0) (8.4.0) Requirement already satisfied: pyparsing>=2.2.1 in /usr/local/lib/python3.9/dist-packages (from matplotlib->tensorflow-gnn==0.1.0) (2.4.7) Requirement already 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satisfied: pyyaml>=5.2 in /usr/local/lib/python3.9/dist-packages (from libcst>=0.2.5->google-cloud-bigquery-storage>=2.6.3->apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (6.0) Requirement already satisfied: importlib-metadata>=4.4 in /usr/local/lib/python3.9/dist-packages (from markdown>=2.6.8->tensorboard~=2.6->tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (4.8.2) Requirement already satisfied: zipp>=0.5 in /usr/local/lib/python3.9/dist-packages (from importlib-metadata>=4.4->markdown>=2.6.8->tensorboard~=2.6->tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (3.6.0) Requirement already satisfied: oauthlib>=3.0.0 in /usr/local/lib/python3.9/dist-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard~=2.6->tensorflow-cpu>=2.7.0->tensorflow-gnn==0.1.0) (3.1.1) Requirement already satisfied: mypy-extensions>=0.3.0 in /usr/local/lib/python3.9/dist-packages (from typing-inspect>=0.4.0->libcst>=0.2.5->google-cloud-bigquery-storage>=2.6.3->apache-beam[gcp]>=2.32->tensorflow-gnn==0.1.0) (0.4.3) Building wheels for collected packages: tensorflow-gnn Building wheel for tensorflow-gnn (setup.py) ... error ERROR: Failed building wheel for tensorflow-gnn Running setup.py clean for tensorflow-gnn Failed to build tensorflow-gnn Installing collected packages: tensorflow-gnn Running setup.py install for tensorflow-gnn ... error ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/content/tensorflow_gnn/setup.py'"'"'; __file__='"'"'/content/tensorflow_gnn/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-qtur1f2t/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.9/tensorflow-gnn Check the logs for full command output.

from gnn.

@lucky630 The message you provided just says an error happened, and we're cleaning some files. The log is too long such that "..." is used in this message.

You may run python3 -m pip install . --log install.log and provide the content of file install.log (especially the error trace in this file).

from gnn.

@lucky630 The message you provided just says an error happened, and we're cleaning some files. The log is too long such that "..." is used in this message.

You may run python3 -m pip install . --log install.log and provide the content of file install.log (especially the error trace in this file).

Thanks, I think it was bazel error after installing bazel 1.0.0 sudo apt install bazel-1.0.0 it was fixed but now I'm getting
AttributeError: module 'tensorflow_gnn' has no attribute 'keras' error

import tensorflow_gnn
dir(tensorflow_gnn)
['__doc__',
 '__file__',
 '__loader__',
 '__name__',
 '__package__',
 '__path__',
 '__spec__']

from gnn.

I'm installing this on Google Colab and for me, the init.py is the same but it still not working

from gnn.

@Maximilianxu
Thanks for your investigation which saved a lot of my time.
It works for me.

from gnn.

Maybe this issue could be pinned so others facing this specific installation error (due to the bazel build) can easily fix it? @sibonli @janpfeifer

The solution is to simply remove the "//tensorflow_gnn/sampler:sampling_spec_pb2.py" line from package/BUILD and run installation step 4 (from the README) again.

from gnn.