Version conflict while installing CIP-Python

[Yonni Friedlander]

Hi all,

While installing CIP, during the CIP-Python install, I get an error message regarding the tensorflow installation.

Specifically, it says: "protobuf requires Python >=3.7."

However, I believe CIP-Python installs python 2.7. I'm a bit out of my depths here and have tried some workarounds but have had no luck

Thanks,

Yonni

[Yonni Friedlander]

Hi,

I'm still running into this issue and was hoping someone here would have experience with it. The full error message is posted below:

[ 84%] Performing installpytables step for 'CIPPython'
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting tensorflow==1.12.0
  Using cached https://files.pythonhosted.org/packages/bd/68/ec26b2cb070a5760707ec8d9491a24e5be72f4885f265bb04abf70c0f9f1/tensorflow-1.12.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting package metadata (current_repodata.json): - Collecting keras-preprocessing>=1.0.5 (from tensorflow==1.12.0)
\   Using cached https://files.pythonhosted.org/packages/79/4c/7c3275a01e12ef9368a892926ab932b33bb13d55794881e3573482b378a7/Keras_Preprocessing-1.1.2-py2.py3-none-any.whl
Requirement already satisfied: enum34>=1.1.6 in ./CIPPython-install/lib/python2.7/site-packages (from tensorflow==1.12.0) (1.1.6)
| Collecting astor>=0.6.0 (from tensorflow==1.12.0)
/   Using cached https://files.pythonhosted.org/packages/c3/88/97eef84f48fa04fbd6750e62dcceafba6c63c81b7ac1420856c8dcc0a3f9/astor-0.8.1-py2.py3-none-any.whl
Collecting backports.weakref>=1.0rc1 (from tensorflow==1.12.0)
-   Using cached https://files.pythonhosted.org/packages/88/ec/f598b633c3d5ffe267aaada57d961c94fdfa183c5c3ebda2b6d151943db6/backports.weakref-1.0.post1-py2.py3-none-any.whl
\ Requirement already satisfied: wheel in ./CIPPython-install/lib/python2.7/site-packages (from tensorflow==1.12.0) (0.33.1)
Collecting mock>=2.0.0 (from tensorflow==1.12.0)
|   Using cached https://files.pythonhosted.org/packages/05/d2/f94e68be6b17f46d2c353564da56e6fb89ef09faeeff3313a046cb810ca9/mock-3.0.5-py2.py3-none-any.whl
/ Collecting tensorboard<1.13.0,>=1.12.0 (from tensorflow==1.12.0)
-   Using cached https://files.pythonhosted.org/packages/51/ae/9840c4837c6f54034ac942b5344396e8c3d74686a9bd29beafdf633cc221/tensorboard-1.12.2-py2-none-any.whl
| Collecting gast>=0.2.0 (from tensorflow==1.12.0)
  Using cached https://files.pythonhosted.org/packages/e4/41/f26f62ebef1a80148e20951a6e9ef4d0ebbe2090124bc143da26e12a934c/gast-0.5.4.tar.gz
\ Collecting termcolor>=1.1.0 (from tensorflow==1.12.0)
|   Using cached https://files.pythonhosted.org/packages/8a/48/a76be51647d0eb9f10e2a4511bf3ffb8cc1e6b14e9e4fab46173aa79f981/termcolor-1.1.0.tar.gz
\ Collecting protobuf>=3.6.1 (from tensorflow==1.12.0)
|   Using cached https://files.pythonhosted.org/packages/6c/be/4e32d02bf08b8f76bf6e59f2a531690c1e4264530404501f3489ca975d9a/protobuf-4.21.0-py2.py3-none-any.whl
/ protobuf requires Python '>=3.7' but the running Python is 2.7.16
- CMakeFiles/CIPPython.dir/build.make:224: recipe for target 'CIPPython-prefix/src/CIPPython-stamp/CIPPython-installtensorflow' failed
make[2]: *** [CIPPython-prefix/src/CIPPython-stamp/CIPPython-installtensorflow] Error 1
make[2]: *** Waiting for unfinished jobs....
done
Solving environment: done

# All requested packages already installed.

CMakeFiles/Makefile2:878: recipe for target 'CMakeFiles/CIPPython.dir/all' failed
make[1]: *** [CMakeFiles/CIPPython.dir/all] Error 2
Makefile:94: recipe for target 'all' failed
make: *** [all] Error 2

Thanks,

Yonni

[San Jose Estepar, Raul,Ph.D.]

Hi Yonni,

We are transition to Python 3.7 but the build process is broken right now.

In the meantime, we provide a dockerized version of CIP that is ready for use: https://hub.docker.com/r/acilbwh/chestimagingplatform

Hopefully this helps to bypass some of the building issues.

Thanks

Raul

On Aug 10, 2023, at 9:51 AM, Yonni Friedlander <yonni.fr...@gmail.com> wrote:

        External Email - Use Caution        

--
You received this message because you are subscribed to the Google Groups "ChestImagingPlatform-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to chestimagingplatfor...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/chestimagingplatform-users/32dc42fa-3db0-48ef-81c1-bd73265983a8n%40googlegroups.com.

The information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline .

Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 

[Yonni Friedlander]

Thank you very much for the reply, Raul. I'll try the docker now.