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glibc version problem with virtualenv #13

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linuxrider opened this issue Feb 14, 2018 · 9 comments
Open

glibc version problem with virtualenv #13

linuxrider opened this issue Feb 14, 2018 · 9 comments

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@linuxrider
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linuxrider commented Feb 14, 2018 •
edited by TingPing
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When I use the snap version (2017.3.3 on Ubuntu 17.10) adding a existing virtualenv works flawlessly.
But not for the flatpak version (2017.3).
There the following dialog pops up:

Cannot set up a python SDK 
at Python 2.7 (python3.6.3-artful) (/home/jo/coding/envs/python3.6.3-artful/bin/python).
The SDK seems invalid.

In the log file:

STDOUT: 
STDERR: /home/jo/coding/envs/python3.6.3-artful/bin/python: /lib/libc.so.6: version `GLIBC_2.25' not found (required by /home/jo/coding/envs/python3.6.3-artful/bin/python)

	at com.jetbrains.python.sdk.PythonSdkType.getSysPathsFromScript(PythonSdkType.java:627)
	at com.jetbrains.python.sdk.PythonSdkType.getSysPath(PythonSdkType.java:610)
	at com.jetbrains.python.sdk.PythonSdkUpdater.evaluateSysPath(PythonSdkUpdater.java:426)
	at com.jetbrains.python.sdk.PythonSdkUpdater.getLocalSdkPaths(PythonSdkUpdater.java:297)
	at com.jetbrains.python.sdk.PythonSdkUpdater.updateLocalSdkPaths(PythonSdkUpdater.java:253)
	at com.jetbrains.python.sdk.PythonSdkUpdater.update(PythonSdkUpdater.java:136)
	at com.jetbrains.python.sdk.PythonSdkUpdater.updateOrShowError(PythonSdkUpdater.java:235)
	at com.jetbrains.python.sdk.PythonSdkType.setupSdkPaths(PythonSdkType.java:515)
	at com.intellij.openapi.projectRoots.impl.SdkConfigurationUtil.setupSdk(SdkConfigurationUtil.java:151)
	at com.jetbrains.python.sdk.PySdkExtKt.setupAssociated(PySdkExt.kt:120)
	at com.jetbrains.python.sdk.add.PyAddExistingVirtualEnvPanel.getOrCreateSdk(PyAddExistingVirtualEnvPanel.kt:56)
	at com.jetbrains.python.sdk.add.PyAddSdkGroupPanel.getOrCreateSdk(PyAddSdkGroupPanel.kt:63)
	at com.jetbrains.python.sdk.add.PyAddSdkDialog.getOrCreateSdk(PyAddSdkDialog.kt:66)
	at com.jetbrains.python.sdk.PythonSdkDetailsStep.createLocalSdk(PythonSdkDetailsStep.java:117)
	at com.jetbrains.python.sdk.PythonSdkDetailsStep.optionSelected(PythonSdkDetailsStep.java:104)
	at com.jetbrains.python.sdk.PythonSdkDetailsStep.lambda$onChosen$0(PythonSdkDetailsStep.java:146)
	at com.intellij.openapi.application.TransactionGuardImpl.performUserActivity(TransactionGuardImpl.java:195)
	at com.intellij.ui.popup.AbstractPopup.lambda$null$7(AbstractPopup.java:1431)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:762)
	at java.awt.EventQueue.access$500(EventQueue.java:98)
	at java.awt.EventQueue$3.run(EventQueue.java:715)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:732)
	at com.intellij.ide.IdeEventQueue.defaultDispatchEvent(IdeEventQueue.java:822)
	at com.intellij.ide.IdeEventQueue._dispatchEvent(IdeEventQueue.java:650)
	at com.intellij.ide.IdeEventQueue.dispatchEvent(IdeEventQueue.java:366)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
	at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:235)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:233)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:233)
	at java.awt.Dialog.show(Dialog.java:1084)
	at com.intellij.openapi.ui.impl.DialogWrapperPeerImpl$MyDialog.show(DialogWrapperPeerImpl.java:734)
	at com.intellij.openapi.ui.impl.DialogWrapperPeerImpl.show(DialogWrapperPeerImpl.java:456)
	at com.intellij.openapi.ui.DialogWrapper.invokeShow(DialogWrapper.java:1696)
	at com.intellij.openapi.ui.DialogWrapper.show(DialogWrapper.java:1645)
	at com.intellij.openapi.options.newEditor.SettingsDialog.lambda$show$0(SettingsDialog.java:83)
	at com.intellij.openapi.application.TransactionGuardImpl.runSyncTransaction(TransactionGuardImpl.java:88)
	at com.intellij.openapi.application.TransactionGuardImpl.submitTransactionAndWait(TransactionGuardImpl.java:153)
	at com.intellij.openapi.options.newEditor.SettingsDialog.show(SettingsDialog.java:83)
	at com.intellij.ide.actions.ShowSettingsUtilImpl.showSettingsDialog(ShowSettingsUtilImpl.java:97)
	at com.intellij.ide.actions.ShowSettingsAction.perform(ShowSettingsAction.java:63)
	at com.intellij.ide.actions.ShowSettingsAction.actionPerformed(ShowSettingsAction.java:52)
	at com.intellij.openapi.actionSystem.ex.ActionUtil$1.run(ActionUtil.java:220)
	at com.intellij.openapi.actionSystem.ex.ActionUtil.performActionDumbAware(ActionUtil.java:237)
	at com.intellij.openapi.actionSystem.impl.ActionMenuItem$ActionTransmitter.lambda$actionPerformed$0(ActionMenuItem.java:321)
	at com.intellij.openapi.wm.impl.FocusManagerImpl.runOnOwnContext(FocusManagerImpl.java:911)
	at com.intellij.openapi.wm.impl.IdeFocusManagerImpl.runOnOwnContext(IdeFocusManagerImpl.java:136)
	at com.intellij.openapi.actionSystem.impl.ActionMenuItem$ActionTransmitter.actionPerformed(ActionMenuItem.java:311)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at com.intellij.openapi.actionSystem.impl.ActionMenuItem.lambda$fireActionPerformed$0(ActionMenuItem.java:130)
	at com.intellij.openapi.application.TransactionGuardImpl.runSyncTransaction(TransactionGuardImpl.java:88)
	at com.intellij.openapi.application.TransactionGuardImpl.lambda$submitTransaction$1(TransactionGuardImpl.java:111)
	at com.intellij.openapi.application.TransactionGuardImpl.submitTransaction(TransactionGuardImpl.java:120)
	at com.intellij.openapi.application.TransactionGuard.submitTransaction(TransactionGuard.java:122)
	at com.intellij.openapi.actionSystem.impl.ActionMenuItem.fireActionPerformed(ActionMenuItem.java:130)
	at com.intellij.ui.plaf.beg.BegMenuItemUI.doClick(BegMenuItemUI.java:521)
	at com.intellij.ui.plaf.beg.BegMenuItemUI.access$300(BegMenuItemUI.java:48)
	at com.intellij.ui.plaf.beg.BegMenuItemUI$MyMouseInputHandler.mouseReleased(BegMenuItemUI.java:541)
	at java.awt.Component.processMouseEvent(Component.java:6541)
	at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
	at java.awt.Component.processEvent(Component.java:6306)
	at java.awt.Container.processEvent(Container.java:2237)
	at java.awt.Component.dispatchEventImpl(Component.java:4897)
	at java.awt.Container.dispatchEventImpl(Container.java:2295)
	at java.awt.Component.dispatchEvent(Component.java:4719)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4889)
	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4526)
	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4467)
	at java.awt.Container.dispatchEventImpl(Container.java:2281)
	at java.awt.Window.dispatchEventImpl(Window.java:2746)
	at java.awt.Component.dispatchEvent(Component.java:4719)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:764)
	at java.awt.EventQueue.access$500(EventQueue.java:98)
	at java.awt.EventQueue$3.run(EventQueue.java:715)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90)
	at java.awt.EventQueue$4.run(EventQueue.java:737)
	at java.awt.EventQueue$4.run(EventQueue.java:735)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:734)
	at com.intellij.ide.IdeEventQueue.defaultDispatchEvent(IdeEventQueue.java:822)
	at com.intellij.ide.IdeEventQueue._dispatchEvent(IdeEventQueue.java:646)
	at com.intellij.ide.IdeEventQueue.dispatchEvent(IdeEventQueue.java:366)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
2018-02-14 06:21:22,736 [ 654947]  ERROR - ns.python.sdk.PythonSdkUpdater - PyCharm 2017.3  Build #PC-173.3727.137 
2018-02-14 06:21:22,736 [ 654947]  ERROR - ns.python.sdk.PythonSdkUpdater - JDK: 1.8.0_152-release 
2018-02-14 06:21:22,736 [ 654947]  ERROR - ns.python.sdk.PythonSdkUpdater - VM: OpenJDK 64-Bit Server VM 
2018-02-14 06:21:22,737 [ 654948]  ERROR - ns.python.sdk.PythonSdkUpdater - Vendor: JetBrains s.r.o 
2018-02-14 06:21:22,737 [ 654948]  ERROR - ns.python.sdk.PythonSdkUpdater - OS: Linux 
2018-02-14 06:21:22,737 [ 654948]  ERROR - ns.python.sdk.PythonSdkUpdater - Last Action: ShowSettings 
2018-02-14 06:21:22,826 [ 655037]   WARN - .python.run.PyVirtualEnvReader - Couldn't read shell environment: rv:1 text:0 out:python: /lib/libc.so.6: version `GLIBC_2.25' not found (required by python)

The python 3.6.3 env is derived from the ubuntu system install.
Seems that python needs access to the systems glibc.
Could this be accomplished?
@TingPing
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Seems that python needs access to the systems glibc.
Could this be accomplished?

No. Any virtual env just must be made in the sandbox not outside.

@linuxrider
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So then it is needed to always create a virtualenv on the base of the python version of the related flatpak platform version?

@TingPing
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Create it from within flatpak, either some graphical tool provided by Pycharm or from the cli: flatpak run --command=sh com.jetbrains.PyCharm-Community

@mhall119
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mhall119 commented Jul 7, 2018

I ran into this same problem. Using @TingPing's command above I was able to get a shell in the Flatpak, however virtualenv isn't installed in it so I had to do the following (inside the Flatpak shell):

  1. pip3 install --user virtualenv, the --user is required because you can't write to /usr/lib/ in the Flatpak
  2. ~/.local/bin/virtualenv --python3 ./env to create a virtualenv using the python3 installed in the Flatpak
  3. ./env/bin/pip install -r requirements to install my dependencies while still in the Flatpak shell

From there I was able to add the virtualenv to my PyCharm settings for my project

@mhall119
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mhall119 commented Jul 7, 2018 •
edited
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BTW, this is needed because /usr/bin/python that PyCharm can see inside the Flatpak environment is different from /usr/bin/python on your host, and it's built against a different version of glibc. A virtualenv created using the host's python won't necessarily be usable using the Flatpak's python.

I think that if the Flatpak were to include the virtualenv executable that PyCharm would be able to create a new virtualenv without problem. I've created issue #29 to do this.

@barthalion
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@mhall119 Verified that it creates virtualenvs correctly now. Can we close the issue?

@mhall119
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I haven't actually verified this yet. I didn't rebuild the flatpak, but I'm assuming it will.

@Red-Eyed
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Red-Eyed commented Apr 1, 2020

You can use conda package manager and install any python version. it will contain libs and does not depend on system libs.

@baudm
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baudm commented Jun 21, 2020

I think all library-loading errors (i.e. "library not found") should be consolidated under #14.

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@barthalion @mhall119 @TingPing @baudm @linuxrider @Red-Eyed