Bug #2704

Updated by Matthieu Decorde 2 months ago

WIP:
In some environments, on Windows, there might be a conflict between already installed R and TXM embedded R.
The bug has been reported on Windows.
Example of R error:

<pre>
Error in readRDS(pfile) :
impossible de lire une version 3 d'un environnement de travail écrit par R 3.6.0 ; besoin d'un R 3.5.0 ou plus récent
</pre>

First diagnostic:
It may be related to the path of libraries that seems to be shared between the both installed R.

TODO:
Add the logs and mail discussions to this issue.

Logs:

*Vérification des packages R : Sortie console TXM :*

<pre>
Vérification des paquets R…org.txm.statsengine.r.core.exceptions.RException: library("textometry"); ** Erreur R : "Error in readRDS(pfile) :
impossible de lire une version 3 d'un environnement de travail écrit par R 3.6.0 ; besoin d'un R 3.5.0 ou plus récent
"
lors de l'évaluation de : try({library("textometry")}, silent=FALSE)
at org.txm.statsengine.r.core.RWorkspace.eval(RWorkspace.java:1119)
at org.txm.statsengine.r.rcp.handlers.CheckRPackages.check(CheckRPackages.java:106)
at org.txm.statsengine.r.rcp.handlers.CheckRPackages.execute(CheckRPackages.java:62)
at org.eclipse.ui.internal.handlers.HandlerProxy.execute(HandlerProxy.java:291)
at org.eclipse.ui.internal.handlers.E4HandlerProxy.execute(E4HandlerProxy.java:92)
... at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:55)
at org.eclipse.e4.core.internal.di.InjectorImpl.invokeUsingClass(InjectorImpl.java:305)
at org.eclipse.e4.core.internal.di.InjectorImpl.invoke(InjectorImpl.java:239)
at org.eclipse.e4.core.contexts.ContextInjectionFactory.invoke(ContextInjectionFactory.java:132)
at org.eclipse.e4.core.commands.internal.HandlerServiceHandler.execute(HandlerServiceHandler.java:152)
at org.eclipse.core.commands.Command.executeWithChecks(Command.java:494)
at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:487)
at org.eclipse.e4.core.commands.internal.HandlerServiceImpl.executeHandler(HandlerServiceImpl.java:210)
at org.eclipse.e4.ui.workbench.renderers.swt.HandledContributionItem.executeItem(HandledContributionItem.java:431)
at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem.handleWidgetSelection(AbstractContributionItem.java:446)
at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem.lambda$2(AbstractContributionItem.java:472)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:86)
at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4428)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1079)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4238)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3817)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$5.run(PartRenderingEngine.java:1150)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1039)
at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:153)
at org.eclipse.ui.internal.Workbench.lambda$3(Workbench.java:680)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:594)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:148)
at org.txm.rcp.Application.start(Application.java:241)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:653)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
at
org.eclipse.equinox.launcher.Main.run(Main.java:1499)
Caused by: org.txm.statsengine.r.core.exceptions.RException: ** Erreur R : "Error in readRDS(pfile) :
impossible de lire une version 3 d'un environnement de travail écrit par R 3.6.0 ; besoin d'un R 3.5.0 ou plus récent
"
lors de l'évaluation de : try({library("FactoMineR")}, silent=FALSE)
at org.txm.statsengine.r.core.RWorkspace.eval(RWorkspace.java:1119)
at org.txm.statsengine.r.rcp.handlers.CheckRPackages.check(CheckRPackages.java:106)
at org.txm.statsengine.r.rcp.handlers.CheckRPackages.execute(CheckRPackages.java:62)
at org.eclipse.ui.internal.handlers.HandlerProxy.execute(HandlerProxy.java:291)
at org.eclipse.ui.internal.handlers.E4HandlerProxy.execute(E4HandlerProxy.java:92)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
... at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:55)
at org.eclipse.e4.core.internal.di.InjectorImpl.invokeUsingClass(InjectorImpl.java:305)
at org.eclipse.e4.core.internal.di.InjectorImpl.invoke(InjectorImpl.java:239)
at org.eclipse.e4.core.contexts.ContextInjectionFactory.invoke(ContextInjectionFactory.java:132)
at org.eclipse.e4.core.commands.internal.HandlerServiceHandler.execute(HandlerServiceHandler.java:152)
at org.eclipse.core.commands.Command.executeWithChecks(Command.java:494)
at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:487)
at org.eclipse.e4.core.commands.internal.HandlerServiceImpl.executeHandler(HandlerServiceImpl.java:210)
at org.eclipse.e4.ui.workbench.renderers.swt.HandledContributionItem.executeItem(HandledContributionItem.java:431)
at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem.handleWidgetSelection(AbstractContributionItem.java:446)
at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem.lambda$2(AbstractContributionItem.java:472)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:86)
at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4428)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1079)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4238)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3817)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$5.run(PartRenderingEngine.java:1150)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1039)
at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:153)
at org.eclipse.ui.internal.Workbench.lambda$3(Workbench.java:680)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:594)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:148)
at org.txm.rcp.Application.start(Application.java:241)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:653)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
at org.eclipse.equinox.launcher.Main.run(Main.java:1499)
Caused by: org.txm.statsengine.r.core.exceptions.RException: ** Erreur R : "Error in readRDS(pfile) :
impossible de lire une version 3 d'un environnement de travail écrit par R 3.6.1 ; besoin d'un R 3.5.0 ou plus récent
"
</pre>

h3. Solution

1- upgrade the R debug macro to show system paths
2- find out if some library paths are shared with another R installation
3- fix R paths

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