Fix libpthread not found during local installation #40706
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Hey @jreback, to be honest I don't know in general, I had to do this to get my development environment working. |
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sure would take that as a note (eg you may have to do this in some platforms) |
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@cgarciae Thanks for checking out pandas and your first PR! Now, I agree we shouldn't just add this. And even instead of adding a note about it, I would first try to understand why this is needed or what's going wrong (eg I am also on Ubuntu 20.04, and using conda environments, but didn't need this). It could also point to something wrong with your conda env (does your conda env have |
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Hey @jorisvandenbossche! I do have |
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This is an odd problem indeed. The conda gcc compiler itself will add even though Pandas doesn't use any multi-threading explicitly (I believe). Can you add a full build log that shows the error in the PR description @cgarciae? |
| @@ -299,6 +299,11 @@ We'll now kick off a three-step process: | |||
| python setup.py build_ext -j 4 | |||
| python -m pip install -e . --no-build-isolation --no-use-pep517 | |||
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| .. note:: | |||
| If the ``python setup.py build_ext -j 4`` command fails on a linux distribution you might | |||
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can we be more specific than "you might be able to"? is there reason to believe this is a common failure mode?
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Can you echo your ldconfig -vvvv variables before you build? |
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Hey @rgommers! I added the logs to the description. |
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One part of the output: So as @rgommers said above, for some reason it is not looking for / not finding libpthread in the conda environment's sysroot. Googling a bit, it seems to come up regularly a while ago (ContinuumIO/anaconda-issues#7363, cocodataset/cocoapi#94), but that was end of 2017 with the migration to new compilers which could give problems. @cgarciae could you also show the output of You could maybe also try to explicitly deactive and reactive the environment, to be sure the env variables are properly set. One of the things mentioned in ContinuumIO/anaconda-issues#7363 is to check |
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Another observation (from ContinuumIO/anaconda-issues#7363 (comment)) that I am seeing here as well: you have So I suppose that's indicating that not all compiler flags are properly set up for the conda env (not fully/correctly activated for some reason?) |
then you are probably building with your system compiler rather than the conda compilers.
I've found that in some cases that's not enough, and you really need a completely fresh terminal. |
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Thanks a lot @jorisvandenbossche and @rgommers! Thanks to your pointers I found the culprit: vscode's terminal seems to do something that makes this happen. I manually activated the conda env from the gnome terminal then ran the previous code and it worked just fine. I'll be closing the issue since it must be something specific to my setup. |
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My previous comment was wrong, I forgot to remove the patch to the |
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Ah that makes sense, environment activation (which sets the sysroot, compilers, etc.) does shell-specific things. |
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@cgarciae you might want to raise an issue at https://github.com/conda/conda to report about the |
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Doing a quick look for their fish support, I actually see https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html#using-with-fish-shell. Did you do |
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@jorisvandenbossche yeah, # >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
eval /home/cristian/miniforge3/bin/conda "shell.fish" "hook" $argv | source
# <<< conda initialize <<<and it works for most stuff but it seems to be failing for this specific use case. I'll post an issue there, thanks for all the help! |
Hey! This is my first PR, I am getting to know the code base and found this as I was doing the local setup.
I was installing the development environment and it was failing due to:
This also happens in the Docker container under some conditions (creating a new env).
Steps followed:
Adding a
extra_link_args.append("-L/usr/lib/x86_64-linux-gnu/")fixed the issue on Ubuntu 20.04.Logs