error with pyenv virtualenv: The SDK seems invalid

[ClonedOne]

I am experiencing a problem with pycharm when trying to select as interpreter a python bin created through a pyenv virtualenv.

Cannot set up a python SDK 
at Python 3.10 (remote_maax) ($HOME/.pyenv/versions/remote_maax/bin/python).
The SDK seems invalid.

I am not using python 3.10, the virtualenv has been created with python 3.8.5. The virtualenv works when activated manually from the shell with pyenv activate, I can pip install packages and use them correcly.

I am on a new install of pop os 20.10 (ubuntu), kernel 5.8.0-7642-generic, pyenv 1.2.22, pycharm community 2020.3.3 installed via flatpak.

Launching pycharm from the shell I get:

com.jetbrains.python.sdk.InvalidSdkException: Failed to determine Python's sys.path value:
STDOUT: 
STDERR: /home/gio/.pyenv/versions/remote_maax/bin/python3.8: /usr/lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (required by /home/gio/.pyenv/versions/remote_maax/bin/python3.8)

    at com.jetbrains.python.sdk.PythonSdkType.getSysPathsFromScript(PythonSdkType.java:457)
    at com.jetbrains.python.sdk.PythonSdkType.getSysPath(PythonSdkType.java:439)
    at com.jetbrains.python.sdk.PythonSdkUpdater.evaluateSysPath(PythonSdkUpdater.java:576)
    at com.jetbrains.python.sdk.PythonSdkUpdater.getLocalSdkPaths(PythonSdkUpdater.java:436)
    at com.jetbrains.python.sdk.PythonSdkUpdater.updateLocalSdkPaths(PythonSdkUpdater.java:400)
    at com.jetbrains.python.sdk.PythonSdkUpdater.updateLocalSdkVersionAndPaths(PythonSdkUpdater.java:370)
    at com.jetbrains.python.sdk.PythonSdkUpdater.lambda$updateVersionAndPathsSynchronouslyAndScheduleRemaining$0(PythonSdkUpdater.java:267)
    at com.intellij.openapi.progress.impl.CoreProgressManager$1.run(CoreProgressManager.java:275)
    at com.intellij.openapi.progress.impl.CoreProgressManager$TaskRunnable.run(CoreProgressManager.java:962)
    at com.intellij.openapi.progress.impl.CoreProgressManager$4.run(CoreProgressManager.java:520)
    at com.intellij.openapi.progress.impl.ProgressRunner.lambda$new$0(ProgressRunner.java:79)
    at com.intellij.openapi.progress.impl.ProgressRunner.lambda$submit$3(ProgressRunner.java:235)
    at com.intellij.openapi.progress.impl.CoreProgressManager.lambda$runProcess$2(CoreProgressManager.java:178)
    at com.intellij.openapi.progress.impl.CoreProgressManager.registerIndicatorAndRun(CoreProgressManager.java:658)
    at com.intellij.openapi.progress.impl.CoreProgressManager.executeProcessUnderProgress(CoreProgressManager.java:610)
    at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:65)
    at com.intellij.openapi.progress.impl.CoreProgressManager.runProcess(CoreProgressManager.java:165)
    at com.intellij.openapi.progress.impl.ProgressRunner.lambda$submit$4(ProgressRunner.java:235)
    at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1700)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.util.concurrent.Executors$PrivilegedThreadFactory$1$1.run(Executors.java:668)
    at java.base/java.util.concurrent.Executors$PrivilegedThreadFactory$1$1.run(Executors.java:665)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at java.base/java.util.concurrent.Executors$PrivilegedThreadFactory$1.run(Executors.java:665)
    at java.base/java.lang.Thread.run(Thread.java:834)

I do have libc 2.32 installed:

glibc-source/groovy,groovy,now 2.32-0ubuntu3 all [installed]
  GNU C Library: sources

libc6/groovy,now 2.32-0ubuntu3 amd64 [installed]
  GNU C Library: Shared libraries

I am posting this here because I have tried doing the same operation with pycharm community downloaded from JetBrains' website (the tarball), and that version works correctly with the same pyenv virtualenv.

Please let me know if I can provide more info to identify the issue

[dotneutron]

I think this is related to #14. @baudm provided what appears to be a fix, although I haven't tried it yet. The problem is due to flatpak's sandboxed nature, as I understand it.

I'm essentially in the same situation, I installed 3.7.10 using pyenv and created a local virtual environment using venv.

You should be able to create a new virtual environment using what I believe is the flatpak's bundled Python version - 3.7.4, but it's not really a solution.

Python 3.7.4 (default, Nov 10 2011, 15:00:00) 
[GCC 9.3.0] on linux

I'm also on glibc 2.32 but the flatpak's bundled glibc seems to be 2.30.

# Run from inside PyCharm's Python Console.
>>> import os; os.system("ldd --version")
ldd (GNU libc) 2.30

It's been mentioned before, but perhaps this is why snap allows the --classic flag for confinement, but flatpak may have different goals in mind. PyCharm (or any IDE for that matter) requires a little more wiggle room.