runtime error for google colab code
dear sir,
I run your colab code but i was given the errors like below at install dependency step.i also ran your colab code one week ago and at that time everything looks fine. i wonder whether you did some updates or do you have some suggestions to fix it?
Found existing installation: jax 0.5.2 Uninstalling jax-0.5.2: Successfully uninstalled jax-0.5.2 Found existing installation: jaxlib 0.5.1 Uninstalling jaxlib-0.5.1: Successfully uninstalled jaxlib-0.5.1 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.3/87.3 MB 8.1 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 17.3 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.1/86.1 MB 8.0 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.5/15.5 MB 2.1 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 MB 1.2 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.9/77.9 kB 2.0 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Building wheel for ml-collections (setup.py) ... done ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 371.0/371.0 kB 8.3 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.4/2.4 MB 39.8 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 105.1/105.1 MB 8.0 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 31.5 MB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Building wheel for pandas (pyproject.toml) ... done ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 7.9 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.3/85.3 kB 2.1 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 152.8/152.8 kB 2.7 MB/s eta 0:00:00 ERROR: Ignored the following yanked versions: 1.11.0, 1.14.0rc1 ERROR: Ignored the following versions that require a different python version: 1.6.2 Requires-Python >=3.7,<3.10; 1.6.3 Requires-Python >=3.7,<3.10; 1.7.0 Requires-Python >=3.7,<3.10; 1.7.1 Requires-Python >=3.7,<3.10; 1.7.2 Requires-Python >=3.7,<3.11; 1.7.3 Requires-Python >=3.7,<3.11; 1.8.0 Requires-Python >=3.8,<3.11; 1.8.0rc1 Requires-Python >=3.8,<3.11; 1.8.0rc2 Requires-Python >=3.8,<3.11; 1.8.0rc3 Requires-Python >=3.8,<3.11; 1.8.0rc4 Requires-Python >=3.8,<3.11; 1.8.1 Requires-Python >=3.8,<3.11 ERROR: Could not find a version that satisfies the requirement scipy==1.7.3 (from versions: 0.8.0, 0.9.0, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.12.1, 0.13.0, 0.13.1, 0.13.2, 0.13.3, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.4.0, 1.4.1, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 1.5.4, 1.6.0, 1.6.1, 1.9.0rc1, 1.9.0rc2, 1.9.0rc3, 1.9.0, 1.9.1, 1.9.2, 1.9.3, 1.10.0rc1, 1.10.0rc2, 1.10.0, 1.10.1, 1.11.0rc1, 1.11.0rc2, 1.11.1, 1.11.2, 1.11.3, 1.11.4, 1.12.0rc1, 1.12.0rc2, 1.12.0, 1.13.0rc1, 1.13.0, 1.13.1, 1.14.0rc2, 1.14.0, 1.14.1, 1.15.0rc1, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2) ERROR: No matching distribution found for scipy==1.7.3 ERROR: Could not find a version that satisfies the requirement tensorflow==2.11.0 (from versions: 2.12.0rc0, 2.12.0rc1, 2.12.0, 2.12.1, 2.13.0rc0, 2.13.0rc1, 2.13.0rc2, 2.13.0, 2.13.1, 2.14.0rc0, 2.14.0rc1, 2.14.0, 2.14.1, 2.15.0rc0, 2.15.0rc1, 2.15.0, 2.15.0.post1, 2.15.1, 2.16.0rc0, 2.16.1, 2.16.2, 2.17.0rc0, 2.17.0rc1, 2.17.0, 2.17.1, 2.18.0rc0, 2.18.0rc1, 2.18.0rc2, 2.18.0, 2.18.1, 2.19.0rc0, 2.19.0) ERROR: No matching distribution found for tensorflow==2.11.0 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 29.4/29.4 MB 42.9 MB/s eta 0:00:00
Hi,
I don't think this should prevent the run? Do you not get any output?
No. Firstly, the installation could not be done correctly. It said the couldn’t find spicy and tensorflow at the required version. After I removed the version require, they are giving error messages when I run your prediction code part. Saying the jax version problems. So no output. But the thing wired me most is that I run your colab code like one week ago. I am pretty sure the code is fine at that time. Could you try to run it again?
More details:
if i remove the version requirement for tensorflow and scipy as below. i got error message like below. i also tried a few different jax versions. but i didnt got anyone working .
AttributeError Traceback (most recent call last)
8 frames /usr/local/lib/python3.11/dist-packages/jax/_src/deprecations.py in getattr(name) 52 message, fn = deprecations[name] 53 if fn is None: # Is the deprecation accelerated? ---> 54 raise AttributeError(message) 55 warnings.warn(message, DeprecationWarning, stacklevel=2) 56 return fn
AttributeError: jax.interpreters.xla.xe was removed in JAX v0.4.36. Use jax.lib.xla_extension instead. On Sun, Mar 16, 2025 at 12:56 PM Patrick Bryant @.***> wrote:
Hi,
I don't think this should prevent the run? Do you not get any output?
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Hi,
I don't think this should prevent the run? Do you not get any output?
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Hi,
I think there are some updates from Google. We will look into it and provide a fix in the coming weeks.
Best,
Patrick
Hi,
It should work now - please try.
Best,
Patrick
Hi,
I think there are some updates from Google. We will look into it and provide a fix in the coming weeks.
Best,
Patrick
I just tried it again, but it's still not working. The issue seems to be unresolved. Could you please check it again? Thanks for your help!
I checked - it works. I think that maybe you are not restarting the runtime after installation? I have added a note about this. "After it finishes (the play button wheel stops spinning) do: Runtime > Restart session (above)."
This seems to be back
There was a problem with fetching the example structure from the PDB. It should be fixed now, please try again.
Best,
Patrick