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Eclipse Wild Web Developer: JavaScript-Typescript Language Server prints error because npm is not included in the flatpak

The following error is printed to the Eclipse's console upon opening a JavaScript/TypeScript file:

[Error] [tsserver] /bin/sh: /app/node/bin/npm: No such file or directory

A fix I did was copy /usr/lib/node_modules/npm into /app/node/, which stops the printing of error.

The error doesn't seem to impact the language server too much though; code analysis still work. But it annoying to get the console filled with error messages.

Eclipse fails to start after flatpak update updating 4.29 release metadata

On fedora 39, I'm running below version of eclipse via flatpak:

Eclipse IDE for Java Developers (includes Incubating components)
Version: 2023-09 (4.29.0)
Build id: 20230907-1323
OS: Linux, v.6.6.6-200.fc39.x86_64, x86_64 / gtk 3.24.38
Java vendor: Eclipse Adoptium
Java runtime version: 17.0.8.1+1
Java version: 17.0.8.1

After a flatpak update, eclipse does not start anymore. Error logs includes below stack trace:

!SESSION 2023-12-19 09:03:23.376 -----------------------------------------------
eclipse.buildId=4.30.0.20231201-1200
java.version=17.0.9
java.vendor=Eclipse Adoptium
BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US
Framework arguments:  -product org.eclipse.epp.package.java.product
Command-line arguments:  -os linux -ws gtk -arch x86_64 -product org.eclipse.epp.package.java.product

!ENTRY org.eclipse.equinox.simpleconfigurator 4 0 2023-12-19 09:03:23.618
!MESSAGE FrameworkEvent ERROR
!STACK 0
org.osgi.framework.BundleException: Exception in org.eclipse.equinox.internal.simpleconfigurator.Activator.start() of bundle org.eclipse.equinox.simpleconfigurator.
	at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:839)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:767)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1032)
	at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:371)
	at org.eclipse.osgi.container.Module.doStart(Module.java:605)
	at org.eclipse.osgi.container.Module.start(Module.java:468)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel$2.run(ModuleContainer.java:1852)
	at org.eclipse.osgi.internal.framework.EquinoxContainerAdaptor$1$1.execute(EquinoxContainerAdaptor.java:136)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1845)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1788)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1750)
	at org.eclipse.osgi.container.SystemModule.startWorker(SystemModule.java:269)
	at org.eclipse.osgi.container.Module.doStart(Module.java:605)
	at org.eclipse.osgi.container.Module.start(Module.java:468)
	at org.eclipse.osgi.container.SystemModule.start(SystemModule.java:193)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.start(EquinoxBundle.java:445)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.start(EquinoxBundle.java:464)
	at org.eclipse.osgi.launch.Equinox.start(Equinox.java:139)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.startup(EclipseStarter.java:338)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:251)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:651)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:588)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1459)
	at org.eclipse.equinox.launcher.Main.main(Main.java:1432)
Caused by: java.lang.IllegalStateException: The System Bundle was updated. The framework must be restarted to finalize the configuration change
	at org.eclipse.equinox.internal.simpleconfigurator.ConfigApplier.install(ConfigApplier.java:79)
	at org.eclipse.equinox.internal.simpleconfigurator.SimpleConfiguratorImpl.applyConfiguration(SimpleConfiguratorImpl.java:189)
	at org.eclipse.equinox.internal.simpleconfigurator.SimpleConfiguratorImpl.applyConfiguration(SimpleConfiguratorImpl.java:204)
	at org.eclipse.equinox.internal.simpleconfigurator.Activator.start(Activator.java:64)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:818)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:1)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:569)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:810)
	... 27 more
Root exception:
java.lang.IllegalStateException: The System Bundle was updated. The framework must be restarted to finalize the configuration change
	at org.eclipse.equinox.internal.simpleconfigurator.ConfigApplier.install(ConfigApplier.java:79)
	at org.eclipse.equinox.internal.simpleconfigurator.SimpleConfiguratorImpl.applyConfiguration(SimpleConfiguratorImpl.java:189)
	at org.eclipse.equinox.internal.simpleconfigurator.SimpleConfiguratorImpl.applyConfiguration(SimpleConfiguratorImpl.java:204)
	at org.eclipse.equinox.internal.simpleconfigurator.Activator.start(Activator.java:64)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:818)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:1)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:569)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:810)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:767)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1032)
	at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:371)
	at org.eclipse.osgi.container.Module.doStart(Module.java:605)
	at org.eclipse.osgi.container.Module.start(Module.java:468)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel$2.run(ModuleContainer.java:1852)
	at org.eclipse.osgi.internal.framework.EquinoxContainerAdaptor$1$1.execute(EquinoxContainerAdaptor.java:136)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1845)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1788)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1750)
	at org.eclipse.osgi.container.SystemModule.startWorker(SystemModule.java:269)
	at org.eclipse.osgi.container.Module.doStart(Module.java:605)
	at org.eclipse.osgi.container.Module.start(Module.java:468)
	at org.eclipse.osgi.container.SystemModule.start(SystemModule.java:193)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.start(EquinoxBundle.java:445)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.start(EquinoxBundle.java:464)
	at org.eclipse.osgi.launch.Equinox.start(Equinox.java:139)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.startup(EclipseStarter.java:338)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:251)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:651)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:588)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1459)
	at org.eclipse.equinox.launcher.Main.main(Main.java:1432)

!ENTRY org.eclipse.osgi 4 0 2023-12-19 09:03:23.619
!MESSAGE Bundle org.eclipse.equinox.simpleconfigurator_1.5.0.v20230919-1457 [1723] is not active.

!ENTRY org.eclipse.osgi 4 0 2023-12-19 09:03:23.624
!MESSAGE Application error
!STACK 1
java.lang.IllegalStateException: Unable to acquire application service. Ensure that the org.eclipse.core.runtime bundle is resolved and started (see config.ini).
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:81)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:402)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:255)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:651)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:588)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1459)
	at org.eclipse.equinox.launcher.Main.main(Main.java:1432)

This error message is very similar to issue #6.

I've tried to run eclipse -clean to no avail:

cd /var/lib/flatpak/exports/bin
./org.eclipse.Java -clean

The only workaround I have found is to revert before the "corrupted" update:

flatpak --version
Flatpak 1.15.6

flatpak remote-info --log flathub org.eclipse.Java

Eclipse IDE for Java Developers - The essential tools for any Java developer,
including a Java IDE, a Git client, XML Editor, Maven and Gradle integration

        ID: org.eclipse.Java
       Ref: app/org.eclipse.Java/x86_64/stable
      Arch: x86_64
    Branch: stable
   Version: 4.30
   License: EPL-2.0
Collection: org.flathub.Stable
  Download: 334.2 MB
 Installed: 390.9 MB
   Runtime: org.gnome.Platform/x86_64/45
       Sdk: org.gnome.Sdk/x86_64/45

    Commit: aecc20258f0abcdba3538c412f472915a54178906155d98a42391396548c8ed1
    Parent: 8619c626d7fef8a849e0ab3167e5cf8c221650303627cf8168b9fbed931511b8
   Subject: Persist the dot folder. (49768643)
      Date: 2023-12-17 12:43:06 +0000
   History: 

    Commit: 8619c626d7fef8a849e0ab3167e5cf8c221650303627cf8168b9fbed931511b8
   Subject: Attempt to associate with eclipse+mpc URIs (03b370a1)
      Date: 2023-12-12 08:55:44 +0000

    Commit: e0f3d2bbbc478fbc01a153238cf561db650ac06c3b02ab77d0fa7b3e1326654d
   Subject: Build for ARM. (6860113a)
      Date: 2023-12-12 07:39:07 +0000

    Commit: 34328ceb5b63fc6c83db5118c1173979131f1d387c79533d168bafbd20278774
   Subject: Update runtime. (c2352ef7)
      Date: 2023-12-11 14:47:37 +0000

    Commit: 62f968a03f7ba326f8a4f83868a0ae1d159b41a6a55aba95c9a6541aadbb996d
   Subject: Add release 4.29 metadata (9c1d7fa7)
      Date: 2023-11-16 10:07:43 +0000

...

sudo flatpak update --commit=62f968a03f7ba326f8a4f83868a0ae1d159b41a6a55aba95c9a6541aadbb996d org.eclipse.Java

With this workaround, it works until next reboot where update is automatically re-applied.

Is a way to fix this ? Or eclipse should be run outside of flatpak ?

Exception when adding plugin repository

When following the instructions here, the flatpak'd Eclipse returns an exception:

eclipse.buildId=4.14.0.I20191020-1800
java.version=11.0.5
java.vendor=Oracle Corporation
BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US
Command-line arguments:  -os linux -ws gtk -arch x86_64

org.eclipse.equinox.p2.ui
Error
Tue Oct 22 11:23:05 EDT 2019
Unable to read repository at https://developer.garmin.com/downloads/connect-iq/eclipse/content.xml.

org.eclipse.equinox.p2.core.ProvisionException: Unable to read repository at https://developer.garmin.com/downloads/connect-iq/eclipse/content.xml.
	at org.eclipse.equinox.internal.p2.repository.CacheManager.createCache(CacheManager.java:247)
	at org.eclipse.equinox.internal.p2.metadata.repository.SimpleMetadataRepositoryFactory.getLocalFile(SimpleMetadataRepositoryFactory.java:69)
	at org.eclipse.equinox.internal.p2.metadata.repository.SimpleMetadataRepositoryFactory.load(SimpleMetadataRepositoryFactory.java:89)
	at org.eclipse.equinox.internal.p2.metadata.repository.MetadataRepositoryManager.factoryLoad(MetadataRepositoryManager.java:63)
	at org.eclipse.equinox.internal.p2.repository.helpers.AbstractRepositoryManager.loadRepository(AbstractRepositoryManager.java:775)
	at org.eclipse.equinox.internal.p2.repository.helpers.AbstractRepositoryManager.loadRepository(AbstractRepositoryManager.java:676)
	at org.eclipse.equinox.internal.p2.metadata.repository.MetadataRepositoryManager.loadRepository(MetadataRepositoryManager.java:110)
	at org.eclipse.equinox.internal.p2.metadata.repository.MetadataRepositoryManager.loadRepository(MetadataRepositoryManager.java:105)
	at org.eclipse.equinox.p2.ui.ProvisioningUI.loadMetadataRepository(ProvisioningUI.java:498)
	at org.eclipse.equinox.internal.p2.ui.model.MetadataRepositoryElement.getMetadataRepository(MetadataRepositoryElement.java:138)
	at org.eclipse.equinox.internal.p2.ui.model.MetadataRepositoryElement.getRepository(MetadataRepositoryElement.java:127)
	at org.eclipse.equinox.internal.p2.ui.model.MetadataRepositoryElement.getQueryable(MetadataRepositoryElement.java:120)
	at org.eclipse.equinox.internal.p2.ui.QueryProvider.getQueryDescriptor(QueryProvider.java:93)
	at org.eclipse.equinox.internal.p2.ui.model.QueriedElement.fetchChildren(QueriedElement.java:104)
	at org.eclipse.equinox.internal.p2.ui.model.MetadataRepositoryElement.fetchChildren(MetadataRepositoryElement.java:86)
	at org.eclipse.equinox.internal.p2.ui.model.RemoteQueriedElement.fetchDeferredChildren(RemoteQueriedElement.java:38)
	at org.eclipse.ui.progress.DeferredTreeContentManager$1.run(DeferredTreeContentManager.java:219)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)
Caused by: javax.net.ssl.SSLException: Unexpected error: java.security.InvalidAlgorithmParameterException: the trustAnchors parameter must be non-empty
	at java.base/sun.security.ssl.Alert.createSSLException(Alert.java:133)
	at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:320)
	at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:263)
	at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:258)
	at java.base/sun.security.ssl.SSLSocketImpl.handleException(SSLSocketImpl.java:1314)
	at java.base/sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:408)
	at org.apache.http.conn.ssl.SSLConnectionSocketFactory.createLayeredSocket(SSLConnectionSocketFactory.java:396)
	at org.apache.http.conn.ssl.SSLConnectionSocketFactory.connectSocket(SSLConnectionSocketFactory.java:355)
	at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:142)
	at org.apache.http.impl.conn.PoolingHttpClientConnectionManager.connect(PoolingHttpClientConnectionManager.java:373)
	at org.apache.http.impl.execchain.MainClientExec.establishRoute(MainClientExec.java:394)
	at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:237)
	at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:185)
	at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:89)
	at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:110)
	at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:185)
	at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:83)
	at org.eclipse.ecf.provider.filetransfer.httpclient45.HttpClientFileSystemBrowser.runRequest(HttpClientFileSystemBrowser.java:246)
	at org.eclipse.ecf.provider.filetransfer.browse.AbstractFileSystemBrowser$DirectoryJob.run(AbstractFileSystemBrowser.java:69)
	... 1 more
Caused by: java.lang.RuntimeException: Unexpected error: java.security.InvalidAlgorithmParameterException: the trustAnchors parameter must be non-empty
	at java.base/sun.security.validator.PKIXValidator.<init>(PKIXValidator.java:89)
	at java.base/sun.security.validator.Validator.getInstance(Validator.java:181)
	at java.base/sun.security.ssl.X509TrustManagerImpl.getValidator(X509TrustManagerImpl.java:300)
	at java.base/sun.security.ssl.X509TrustManagerImpl.checkTrustedInit(X509TrustManagerImpl.java:176)
	at java.base/sun.security.ssl.X509TrustManagerImpl.checkTrusted(X509TrustManagerImpl.java:189)
	at java.base/sun.security.ssl.X509TrustManagerImpl.checkServerTrusted(X509TrustManagerImpl.java:129)
	at java.base/sun.security.ssl.CertificateMessage$T13CertificateConsumer.checkServerCerts(CertificateMessage.java:1308)
	at java.base/sun.security.ssl.CertificateMessage$T13CertificateConsumer.onConsumeCertificate(CertificateMessage.java:1199)
	at java.base/sun.security.ssl.CertificateMessage$T13CertificateConsumer.consume(CertificateMessage.java:1146)
	at java.base/sun.security.ssl.SSLHandshake.consume(SSLHandshake.java:392)
	at java.base/sun.security.ssl.HandshakeContext.dispatch(HandshakeContext.java:443)
	at java.base/sun.security.ssl.HandshakeContext.dispatch(HandshakeContext.java:421)
	at java.base/sun.security.ssl.TransportContext.dispatch(TransportContext.java:177)
	at java.base/sun.security.ssl.SSLTransport.decode(SSLTransport.java:164)
	at java.base/sun.security.ssl.SSLSocketImpl.decode(SSLSocketImpl.java:1152)
	at java.base/sun.security.ssl.SSLSocketImpl.readHandshakeRecord(SSLSocketImpl.java:1063)
	at java.base/sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:402)
	... 14 more
Caused by: java.security.InvalidAlgorithmParameterException: the trustAnchors parameter must be non-empty
	at java.base/java.security.cert.PKIXParameters.setTrustAnchors(PKIXParameters.java:200)
	at java.base/java.security.cert.PKIXParameters.<init>(PKIXParameters.java:120)
	at java.base/java.security.cert.PKIXBuilderParameters.<init>(PKIXBuilderParameters.java:104)
	at java.base/sun.security.validator.PKIXValidator.<init>(PKIXValidator.java:86)
	... 30 more

On IRC, you mentioned this may be because it's an old (v1?) plugin repository.

Installation fails

I'm following the installation instructions from http://eclipse.matbooth.co.uk/flatpak/ but installation fails for me.

vogella@spike:~$ flatpak install eclipse-nightly org.eclipse.Sdk
Required runtime for org.eclipse.Sdk/x86_64/Photon (org.gnome.Platform/x86_64/3.28) is not installed, searching...
The required runtime org.gnome.Platform/x86_64/3.28 was not found in a configured remote.
error: The Application org.eclipse.Sdk/x86_64/Photon requires the runtime org.gnome.Platform/x86_64/3.28 which is not installed

Occasionally installed bundles no longer detected by Equinox at startup

Eclipse SDK
Version: 2019-03 (4.11)
Build id: I20190211-1800

Occasionally, I'll start up the flatpak Eclipse instance and noticed that the bundles I had installed (through features) no longer contribute to the UI. A few other things I've noticed when this happens :

  • Looking at the OSGi console I also see they are not present.
  • I see the features in Installation Details -> Installed Software, and even the Installation History seems to show their existence, but they're not under Features or Plug-ins
  • I see the bundles in the $HOME/.var/app/org.eclipse.Sdk/eclipse/configuration/org.eclipse.equinox.simpleconfigurator/bundles.info

I'm not sure the exact conditions necessary to reproduce this (though I suspect perhaps this happens after a flatpak update). There have been times when flatpak update triggers remediation to re-install the features and it all works fine afterwards.

Can eclipse flatpak be somehow linked to org.freedesktop.Sdk?

Hello, I wanted to try to write a small c++ program in Eclipse flatpak, but I can't compile it, since Eclipse can't find gcc compiler. I have gcc compiler installed inside org.freedesktop.Sdk and it works fine with Codeblocks flatpak. Is it somehow possible to allow Eclipse flatpak to use org.freedesktop.Sdk binaries (including gcc)?

Hovering over any java source element causes WebKitWebProcess crash

Fedora release 28 (Twenty Eight)
Eclipse SDK
Version: 2018-12 (4.10)
Build id: I20181010-0600

The executable seems to be /usr/libexec/webkit2gtk-4.0/WebKitWebProcess . I also recall running into this prior to updating to the 2018-12 flatpak.

Hovering over the element does bring up the shell, but the content isn't populated.

Eclipse fails to start after flatpak update

Steps to reproduce:

  1. Run eclipse platform from flatpak
  2. Enable http://download.eclipse.org/eclipse/updates/4.8-I-builds/ repo
  3. Install SWT Tools, Releng tools, EEs and various other components
  4. On the next Eclipse platform update via flatpak it fails to start and creates ~/.var/app/org.eclipse.Platform/eclipse/configuration/*.log files with the following content:
!SESSION 2018-04-11 11:03:30.019 -----------------------------------------------
eclipse.buildId=4.8.0.I20180409-2000
java.version=9
java.vendor=Oracle Corporation
BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US
Command-line arguments:  -os linux -ws gtk -arch x86_64 -clean

!ENTRY org.eclipse.equinox.simpleconfigurator 4 0 2018-04-11 11:03:30.488
!MESSAGE FrameworkEvent ERROR
!STACK 0
org.osgi.framework.BundleException: Exception in org.eclipse.equinox.internal.simpleconfigurator.Activator.start() of bundle org.eclipse.equinox.simpleconfigurator.
	at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:800)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:729)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1002)
	at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:354)
	at org.eclipse.osgi.container.Module.doStart(Module.java:581)
	at org.eclipse.osgi.container.Module.start(Module.java:449)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1682)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1662)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1624)
	at org.eclipse.osgi.container.SystemModule.startWorker(SystemModule.java:264)
	at org.eclipse.osgi.container.Module.doStart(Module.java:581)
	at org.eclipse.osgi.container.Module.start(Module.java:449)
	at org.eclipse.osgi.container.SystemModule.start(SystemModule.java:188)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.start(EquinoxBundle.java:428)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.start(EquinoxBundle.java:447)
	at org.eclipse.osgi.launch.Equinox.start(Equinox.java:115)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.startup(EclipseStarter.java:326)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:239)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:564)
	at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:656)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:592)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1498)
	at org.eclipse.equinox.launcher.Main.main(Main.java:1471)
Caused by: java.lang.IllegalStateException: The System Bundle was updated. The framework must be restarted to finalize the configuration change
	at org.eclipse.equinox.internal.simpleconfigurator.ConfigApplier.install(ConfigApplier.java:80)
	at org.eclipse.equinox.internal.simpleconfigurator.SimpleConfiguratorImpl.applyConfiguration(SimpleConfiguratorImpl.java:192)
	at org.eclipse.equinox.internal.simpleconfigurator.SimpleConfiguratorImpl.applyConfiguration(SimpleConfiguratorImpl.java:207)
	at org.eclipse.equinox.internal.simpleconfigurator.Activator.start(Activator.java:61)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:779)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:772)
	... 25 more
Root exception:
java.lang.IllegalStateException: The System Bundle was updated. The framework must be restarted to finalize the configuration change
	at org.eclipse.equinox.internal.simpleconfigurator.ConfigApplier.install(ConfigApplier.java:80)
	at org.eclipse.equinox.internal.simpleconfigurator.SimpleConfiguratorImpl.applyConfiguration(SimpleConfiguratorImpl.java:192)
	at org.eclipse.equinox.internal.simpleconfigurator.SimpleConfiguratorImpl.applyConfiguration(SimpleConfiguratorImpl.java:207)
	at org.eclipse.equinox.internal.simpleconfigurator.Activator.start(Activator.java:61)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:779)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:772)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:729)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1002)
	at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:354)
	at org.eclipse.osgi.container.Module.doStart(Module.java:581)
	at org.eclipse.osgi.container.Module.start(Module.java:449)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1682)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1662)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1624)
	at org.eclipse.osgi.container.SystemModule.startWorker(SystemModule.java:264)
	at org.eclipse.osgi.container.Module.doStart(Module.java:581)
	at org.eclipse.osgi.container.Module.start(Module.java:449)
	at org.eclipse.osgi.container.SystemModule.start(SystemModule.java:188)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.start(EquinoxBundle.java:428)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.start(EquinoxBundle.java:447)
	at org.eclipse.osgi.launch.Equinox.start(Equinox.java:115)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.startup(EclipseStarter.java:326)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:239)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:564)
	at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:656)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:592)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1498)
	at org.eclipse.equinox.launcher.Main.main(Main.java:1471)

!ENTRY org.eclipse.osgi 4 0 2018-04-11 11:03:30.493
!MESSAGE Bundle org.eclipse.equinox.simpleconfigurator_1.3.0.v20180119-2027 [2] is not active.

!ENTRY org.eclipse.osgi 4 0 2018-04-11 11:03:30.496
!MESSAGE Application error
!STACK 1
java.lang.IllegalStateException: Unable to acquire application service. Ensure that the org.eclipse.core.runtime bundle is resolved and started (see config.ini).
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:78)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:564)
	at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:656)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:592)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1498)
	at org.eclipse.equinox.launcher.Main.main(Main.java:1471)

Eclipse fails to start after flatpak update from March 10th

Hello, the issue is the same nature as of #16 .

After the update from March 10th, eclipse can't start with below error log:

org.osgi.framework.BundleException: Exception in org.eclipse.equinox.internal.simpleconfigurator.Activator.start() of bundle org.eclipse.equinox.simpleconfigurator.
	at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:854)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:775)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1057)
	at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:387)
	at org.eclipse.osgi.container.Module.doStart(Module.java:639)
	at org.eclipse.osgi.container.Module.start(Module.java:498)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel$2.run(ModuleContainer.java:2073)
	at org.eclipse.osgi.internal.framework.EquinoxContainerAdaptor$1$1.execute(EquinoxContainerAdaptor.java:143)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:2064)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:2006)
	at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1967)
	at org.eclipse.osgi.container.SystemModule.startWorker(SystemModule.java:274)
	at org.eclipse.osgi.container.Module.doStart(Module.java:639)
	at org.eclipse.osgi.container.Module.start(Module.java:498)
	at org.eclipse.osgi.container.SystemModule.start(SystemModule.java:198)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.start(EquinoxBundle.java:463)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.start(EquinoxBundle.java:482)
	at org.eclipse.osgi.launch.Equinox.start(Equinox.java:139)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.startup(EclipseStarter.java:367)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:267)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:651)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:588)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1459)
	at org.eclipse.equinox.launcher.Main.main(Main.java:1432)
Caused by: java.lang.IllegalStateException: The System Bundle was updated. The framework must be restarted to finalize the configuration change
	at org.eclipse.equinox.internal.simpleconfigurator.ConfigApplier.install(ConfigApplier.java:93)
	at org.eclipse.equinox.internal.simpleconfigurator.SimpleConfiguratorImpl.applyConfiguration(SimpleConfiguratorImpl.java:189)
	at org.eclipse.equinox.internal.simpleconfigurator.SimpleConfiguratorImpl.applyConfiguration(SimpleConfiguratorImpl.java:204)
	at org.eclipse.equinox.internal.simpleconfigurator.Activator.start(Activator.java:63)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:833)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:1)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:569)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:825)
	... 27 more

It's possible to workaround with rollback to previous version:

sudo flatpak update --commit=aecc20258f0abcdba3538c412f472915a54178906155d98a42391396548c8ed1 org.eclipse.Java

org.eclipse.Sdk from eclipse-nightly hangs on installing plugins

  1. $ flatpak run org.eclipse.Sdk and select a new workspace
  2. Help -> Install New Software...
  3. Select "All Available Sites", filter for 'git' and install 'Git integration for Eclipse'
  4. Hit next through the install details / license review, accept the license and click Finish

I seem to recall this wasn't an issue when I tried the Oxygen.1 runtime.

Can not run make

Create a hello world ansi c project. Try to compile it.

09:25:11 **** Build of configuration Debug for project testc2 ****
make all 
Cannot run program "make": Unknown reason

Error: Program "make" not found in PATH
PATH=[/app/bin:/usr/bin]

09:25:11 Build Failed. 1 errors, 0 warnings. (took 2ms)

Defaults in eclipse.ini

The default memory allocation with the flatpak is:
-Xms40m
-Xmx512m
This is too low for several of my workspaces, can you adjust to:
-Xms512m
-Xmx2048m
Or even better, is there some way to override this? Ideally in the eclipse.ini, but I can't locate it in the flatpak?

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