Comments (15)
endrebak
commented on June 2, 2024
Thanks. Will fix this by a refactoring as soon as I get back on Monday. I
know what the problem is :)
…On Friday, April 19, 2019, Simo Zhang ***@***.***> wrote:
Hello,
Thanks very much for bringing GRanges to python. Very much appreciated!
I tried to install pyranges through pip install pyranges. The
installation issued no problems. However, when I tried to import pyranges,
it complained about No module named raymock.
I did a quick fix by updating import pyranges.ramock as ray as import
ramock as ray in the pyranges.py. But then it similarly complained other
packages. I am wondering is there way I can just fix all automatically?
Thanks for any help.
Simo
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endrebak
commented on June 2, 2024
What are the exact commands that made it fail? I want to see if I can
reproduce the error. Anyways, this is going to be fixed by a refactoring I
had planned anyways.
You could try pip install ray, import ray before you import pyranges and
see if it works. I did not want to have ray as a dependency for the
project, so I made a raymock library. But the current way I have of dealing
with the missing dependency is obviously not working too well.
Note to self: think of some ways of testing this :)
Endre
On Saturday, April 20, 2019, Endre Bakken Stovner <[email protected]>
wrote:
… Thanks. Will fix this by a refactoring as soon as I get back on Monday. I
know what the problem is :)
On Friday, April 19, 2019, Simo Zhang ***@***.***> wrote:
> Hello,
>
> Thanks very much for bringing GRanges to python. Very much appreciated!
>
> I tried to install pyranges through pip install pyranges. The
> installation issued no problems. However, when I tried to import pyranges,
> it complained about No module named raymock.
>
> I did a quick fix by updating import pyranges.ramock as ray as import
> ramock as ray in the pyranges.py. But then it similarly complained other
> packages. I am wondering is there way I can just fix all automatically?
> Thanks for any help.
>
> Simo
>
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> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#5>, or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AEHURUTSNLGAUSTLYS7SYQLPRE5M5ANCNFSM4HHBYCGA>
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>
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svm-zhang
commented on June 2, 2024
Thanks very much for getting back to me!
I followed your suggestions on install ray and import it before importing pyranges. However, import ray complains a GLIBC conflict I think. The error message is:
/lib64/libc.so.6: version GLIBC_2.14' not found`
I am using anaconda and it has a gcc 7.3.0. Not sure how I should get pass this one :)
Simo
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endrebak
commented on June 2, 2024
So I really should not require ray then. I will fix this on Monday. I have
many ideas.
Btw you did not call your file pyranges or have a pyranges dir in the dir
you tried to run the file from? That could lead to your original error too.
But the code you found an error in is not robust and will be fixed Monday.
…On Sunday, April 21, 2019, Simo Zhang ***@***.***> wrote:
Thanks very much for getting back to me!
I followed your suggestions on install ray and import it before importing
pyranges. However, import ray complains a GLIBC conflict I think. The
error message is:
/lib64/libc.so.6: version GLIBC_2.14' not found`
I am using anaconda and it has a gcc 7.3.0. Not sure how I should get pass
this one :)
Simo
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svm-zhang
commented on June 2, 2024
Thats correct. I tried to import pyranges from any generic location within which there was no pyranges dir. Looking forward to the fix :) Thanks!
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endrebak
commented on June 2, 2024
Could you please try pip install --no-cache-dir pyranges? Should be fixed now :)
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endrebak
commented on June 2, 2024
To prevent similar things from happening I will set up tests with tox so that pyranges can be tested under different environments (for example with/without ray).
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svm-zhang
commented on June 2, 2024
You are lighting fast on fixing this :)
The installation of v0.0.28 was successful. The error now is a similar one:from pyrnages.tostring import tostring: No module named tostring.
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endrebak
commented on June 2, 2024
Is the spelling error yours (pyrnages)? :) Or is it copy and paste?
Anyways, what Python version are you using? I do not support legacy Python (version2), only Python 3.5 and up (3.4 was deprecated in March).
How did you install pyranges? I just did pip install pyranges==0.0.28 and it works fine. It also works on TRAVIS.
What is your environment? macOS/Windows/Linux?
What commands did you try? :)
Thanks for getting back to me so quickly.
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svm-zhang
commented on June 2, 2024
Haha, thats my typo...
I see the problem now. I am using python 2.7.15. Do you think there is a way I can get pass this?
Simo
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endrebak
commented on June 2, 2024
Download another version of python. Just google anaconda and you will find
a great installer :) I should add something to setup.py to notify 2.7
people that their python is not supported.
…On Tuesday, April 23, 2019, Simo Zhang ***@***.***> wrote:
Haha, thats my typo...
I see the problem now. I am using python 2.7.15. Do you think there is a
way I can get pass this?
Simo
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svm-zhang
commented on June 2, 2024
I have the anaconda python 2.7 env installed. Gonna have to deal with a different env if I install python 3 :). Anyway, I will try to install using a python3 env and report back. Thanks!
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endrebak
commented on June 2, 2024
Yeah, Python2.7 is soon retiring: https://pythonclock.org/
And many of the libraries I depend on are not even updated for 2.7 anymore
so even if I wanted to make PyRanges work with 2.7 I would not be able to
:)
…On Tue, Apr 23, 2019 at 9:47 PM Simo Zhang ***@***.***> wrote:
I have the anaconda python 2.7 env installed. Gonna have to deal with a
different env if I install python 3 :). Anyway, I will try to install using
a python3 env and report back. Thanks!
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svm-zhang
commented on June 2, 2024
True.
I can confirm it works perfectly fine once I switched to python 3. Thanks for being such a great help.
Simo
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endrebak
commented on June 2, 2024
Thanks for reporting. I really needed to fix the ray stuff anyways :)
…On Wednesday, April 24, 2019, Simo Zhang ***@***.***> wrote:
Closed #5 <#5>.
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